SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cummeRbund ANDing in getSig Starr_Hazard Bioinformatics 9 07-26-2012 12:29 PM
Water stress and Mycorrhization - Alpha diversity conclusions?? Chuckytah RNA Sequencing 2 07-04-2012 02:16 PM
getSig function in cummerBund shurjo Bioinformatics 3 04-25-2012 11:57 AM
Scripture Alpha Version? SamCurt Bioinformatics 0 12-24-2011 06:39 AM

Reply
 
Thread Tools
Old 03-08-2013, 08:22 AM   #1
cnyh
Member
 
Location: Norway

Join Date: Feb 2013
Posts: 39
Default cummeRbund getSig(): alpha?

I've used the following command to extract significant genes:

mySigGenes <- getSig(cuff, alpha = 0.05, level = "genes")

However, I don't understand why terms familiar to me such as "FPKM" and "q-value" are not arguments in this filtering process. Also, what does "alpha" mean?
cnyh is offline   Reply With Quote
Old 03-08-2013, 09:58 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
Default

P-value http://en.wikipedia.org/wiki/P-value.
GenoMax is offline   Reply With Quote
Old 03-08-2013, 10:00 AM   #3
cnyh
Member
 
Location: Norway

Join Date: Feb 2013
Posts: 39
Default

Ah, I see. So alpha is the cutoff for the p-value then. Does the same apply for q-value as well?
cnyh is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:48 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO